From 9001945de8f366d4bb205e415b5d3334e29a04c6 Mon Sep 17 00:00:00 2001 From: Ajit Johnson Nirmal Date: Fri, 15 Mar 2024 10:42:08 -0400 Subject: [PATCH] added to index --- docs/Tools Shortcut.md | 1 + scimap/plotting/heatmap.py | 8 ++++---- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/docs/Tools Shortcut.md b/docs/Tools Shortcut.md index 51ae978e..f189dd63 100644 --- a/docs/Tools Shortcut.md +++ b/docs/Tools Shortcut.md @@ -50,6 +50,7 @@ import scimap as sm | [`sm.pl.image_viewer`](Functions/pl/image_viewer.md) | Integrates with `napari` to offer an interactive platform for enhanced image viewing and annotation with data overlays. | | [`sm.pl.addROI_image`](Functions/pl/addROI_image.md) | Facilitates the addition of Regions of Interest (ROIs) through `napari`, enriching spatial analyses with precise locational data. | | [`sm.pl.gate_finder`](Functions/pl/gate_finder.md) | Aids in the manual gating process by overlaying marker positivity on images, simplifying the identification and analysis of cellular subsets. | +| [`sm.pl.heatmap`](Functions/pl/heatmap.md) | Creates heatmaps to visually explore marker expression or feature distributions across different groups. | | [`sm.pl.distPlot`](Functions/pl/distPlot.md) | Generates distribution plots for specific markers, allowing for the visual comparison of marker expression across different conditions or cell types. | | [`sm.pl.densityPlot2D`](Functions/pl/densityPlot2D.md) | Creates two-dimensional density plots of marker expressions, facilitating the visualization of expression patterns and densities in a spatial context. | | [`sm.pl.cluster_plots`](Functions/pl/cluster_plots.md) | Provides a meta-function that outputs a combination of UMAP, heatmap, and ranked markers for each group, offering a comprehensive view of clustering results. | diff --git a/scimap/plotting/heatmap.py b/scimap/plotting/heatmap.py index e0920ffd..9cd322fc 100644 --- a/scimap/plotting/heatmap.py +++ b/scimap/plotting/heatmap.py @@ -102,13 +102,13 @@ def heatmap (adata, Returns a plot, if `saveDir` and `fileName` are provided, the plot is saved in the given directory. Example: - ```python + ```python - Example 1: Basic usage with clustering and standard scale by column. + # Example 1: Basic usage with clustering and standard scale by column. sm.pl.heatmap(adata, groupBy='leiden', standardScale='column') - Example 2: Advanced usage with specified subset markers, custom grouping, and file saving. + # Example 2: Advanced usage with specified subset markers, custom grouping, and file saving. subsetMarkers = ['ELANE', 'CD57', 'CD45', 'CD11B', 'SMA', 'CD16', 'ECAD'] subsetGroups = ['0', '1', '3', '6'] @@ -119,7 +119,7 @@ def heatmap (adata, sm.pl.heatmap(adata, groupBy='leiden', subsetMarkers=subsetMarkers, subsetGroups=subsetGroups, clusterRows=False, clusterColumns=False, standardScale='column', orderRow=orderRow, orderColumn=orderColumn, showPrevalence=True, figsize=(10, 5), saveDir=saveDir, fileName=fileName, vmin=0, vmax=1) - ``` + ``` """ # load adata